I'm not sure that this is what Dave has in mind, but if anyone is
interested in simulating bounded evolution in R, I just added it to my
"fastBM()" function (code here:
http://anolis.oeb.harvard.edu/~liam/R-phylogenetics/fastBM/v0.3/fastBM.R).
In the process of evolving traits up the tree, I just bounce back any
phenotypes that exceed the lower or upper boundary conditions specified
by the user (by default they are -Inf and Inf). I think I did this
properly. Feedback welcome though.
- Liam
--
Liam J. Revell
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
(new) email: liam.rev...@umb.edu
(new) blog: http://phytools.blogspot.com
On 3/5/2011 12:55 PM, tgarl...@ucr.edu wrote:
Hello David, Enrico, et al.,
I may have lost track of what Dave was originally trying to do, and I am not
familiar with all of the options presently available in r for simulating
continuously valued traits along a specified phylogenetic tree. However, I
wanted to point out that MANY possibilities, including trends, the OU process,
and actual limits to trait evolution implemented in several ways, are available
in our original DOS program PDSIMUL.EXE that accompanies this paper:
Garland, T., Jr., A. W. Dickerman, C. M. Janis, and J. A. Jones. 1993.
Phylogenetic analysis of covariance by computer simulation. Systematic Biology
42:265-292.
It has been used many times to look at trends, limits, etc., e.g., in these
papers:
Díaz-Uriarte, R., and T. Garland, Jr. 1996. Testing hypotheses of correlated
evolution using phylogenetically independent contrasts: sensitivity to
deviations from Brownian motion. Systematic Biology 45:27-47.
Laurin, M. 2010. Assessment of the relative merits of a few methods to detect
evolutionary trends. Syst. Biol. 59:689-704.
Cheers,
Ted
Theodore Garland, Jr.
Professor
Department of Biology
University of California, Riverside
Riverside, CA 92521
Office Phone: (951) 827-3524
Lab Phone: (951) 827-5724
Home Phone: (951) 328-0820
Facsimile: (951) 827-4286 = Dept. office (not confidential)
Email: tgarl...@ucr.edu
Main Departmental page:
http://www.biology.ucr.edu/people/faculty/Garland.html
List of all Publications:
http://www.biology.ucr.edu/people/faculty/Garland/GarlandPublications.html
Garland and Rose, 2009
http://www.ucpress.edu/books/pages/10604.php
---- Original message ----
Date: Sat, 05 Mar 2011 15:36:13 +0100
From: Enrico Rezende<enrico.reze...@uab.cat>
Subject: Re: [R-sig-phylo] Dealing with Bounded Trait Measures
To: David Bapst<dwba...@uchicago.edu>
Cc: R Sig Phylo Listserv<r-sig-phylo@r-project.org>
>David,
>on the top of my head, if no species measurement strictly
corresponds to
>zero, you may log-transform the data. You may then simulate
Brownian
>motion in log-transformed values, which will correspond to a
boundary of
>zero in a linear scale (i.e., the more negative the log number, the
>closer the trait value is to zero - but never zero - in a linear
scale).
>This also explains why you can simulate the evolution of body mass
>employing Brownian motion in log-transformed units and no species
will
>ever be assigned a body mass of zero. On more speculative grounds,
this
>may simply reflect the fact that many biological processes and
their
>regulation occur in a multiplicative, not additive, scale.
>
>The problem with regards to this approach is that you cannot really
have
>any species with a trait = 0 given that the log-transformation is
>impossible in this case, so you might add some constant in case
this
>occurs (caution because the constant would be arbitrary and might
have
>an impact on the outcome of analyses). Did not think about this for
too
>long, though.
>
>Hope this helps,
>Enrico
>
>
>
>
>
>El 4/3/11 9:14 p.m., David Bapst escribió:
>> All-
>> As far as I understand it, the vast majority of continuous
character
>> analyses assume that the trait is distributed normally and
without
>> bounds. Is there an appropriate transformation to for
measurements of
>> a trait that does have one or more bounds and where some taxa
actually
>> are at that bound? I have several traits where the bound is zero,
and
>> some taxa are actually at zero for this trait. (A practical
example is
>> 'spine length', where some taxa have virtually no spine.) And if
there
>> is no transformation applicable, is it analytically appropriate
to
>> remove taxa that have 'zero units' for that trait? Must we
convert
>> these traits to discrete categories to deal with them at all?
>>
>> As always, I appreciate your advice.
>> -Dave Bapst, UChicago
>>
>
>
>--
>************************************************************************
>Enrico L. Rezende
>
>Departament de Genètica i de Microbiologia
>Facultat de Biociències, Edifici Cn
>Universitat Autònoma de Barcelona
>08193 Bellaterra (Barcelona)
>SPAIN
>
>Telephone: +34 93 581 4705
>Fax: +34 93 581 2387
>E-mail: enrico.reze...@uab.cat
>
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